MAGE's animation of deoxy to carbonmonoxy transition
of heme in hemoglobin (Protour8.kin).
After 25 cycles, animation will stop. Reload to reanimate.
MAGE can show different conformations of a molecule. For example, it can show the effect of substrate occupancy on the conformation of the active site of an enzyme. This "molecular animation" capability of MAGE is something which RasMol does not provide. Such conformational changes can, however, be toggled or morphed in Chime as pseudo-NMR files, or animated as XYZ files (see the animated thermal vibrations mapped to peaks in an infrared spectrum, for example).
RasMol and MAGE have some overlap in capabilities, but are designed for different purposes and are largely complementary. MAGE is designed to show views and transformations selected by the author of a MAGE script. It provides a series of buttons to move through the author-selected views and transformations. MAGE provides a graphics window, a caption window, a control panel, and a text window. MAGE lends itself to extensive teaching tutorials. In contrast, RasMol lends itself more to free-roaming, user-initiated exploration of molecular structures. MAGE provides a limited set of molecular representations, largely of the "stick figure" type, whereas RasMol provides a much wider range of representations (space-filling, cartoon, ribbon, backbone, stick, ball and stick, etc.).
MAGE is not limited to molecular structures; it can in fact be used to present a variety of three-dimensional information. An example provided with MAGE shows the steps in the construction of a geodesic dome. Another example shows a three-dimensional graph of data. These can be rotated at will, and viewed in stereo.
MAGE and kinemages were first described in "The kinemage: a tool for scientific communication" by David C. Richardson and Jane S. Richardson, Protein Sci 1992 Jan;1(1):3-9. Until 1997 (?), each issue of the journal Protein Science was accompanied with a diskette of kinemages to illustrate findings published in that issue.
Kinemage scripts for MAGE are prepared with another free program called PreKin. These are more technical to prepare than are scripts for RasMol. RasMol's write kinemage filename command writes the equivalent of a RasMol script in MAGE format. From such a script, MAGE will start with the desired view of a molecule, appropriately colored and represented. This is one way to start a MAGE script which can then be manually modified to use MAGE's special features.
Any two molecules can be aligned and the alignment viewed in MAGE using an automated kinemage-generation routine at NCBI Entrez. To do this, use Structure Query, then choose one molecule and select Structure Summary, and on this page, Structure Neighbors. Check one chain in the neighbors list checkbox, select MAGE as the viewer, Options Launch Viewer, and press the View Alignments button. If your browser is not configured to spawn MAGE automatically, use the Pick App option on the Unknown File Type dialog and browse to your copy of MAGE.
Additional comparison of RasMol and MAGE is made in the page on History of Visualization of Biological Macromolecules.